Should I package my issue for background download into one large file, or download each asset separately?
Packaging your issue assets into one compressed file is best for system performance, and it lets you determine the total download time for your issue.
Since your app has to be woken up and notified whenever a download finishes, downloading each issue asset individually is not the best approach for system performance. And, when you download each asset individually, it's impossible to calculate the total download time for your issue.
If you cannot deliver your issue in a single compressed file, then you should group your assets into sets of downloads that make sense for your app. For example, you might group the assets that are needed to show the first page of your issue into a single download.